Comparative transcriptomic and rhizosphere microbiome profiling and cross-omics association analysis of wild and cultivated

Introduction: Methods: Transcriptomic and rhizosphere microbiome analyses were conducted in sampled wild and cultivated populations, followed by an exploratory cross-omics association analysis. Results: Transcriptome comparisons identified 10,416, 8,782, and 5,441 differentially expressed unigenes in roots, rhizomes, and leaves, respectively. Functional enrichment analyses showed differences in plant hormone signal transduction, MAPK signaling, plant-pathogen interaction, phenylpropanoid biosynthesis, and terpenoid biosynthesis pathways. Several terpenoid biosynthesis-related genes, including AACT, HMGS, HMGR, DXS, and TPS, had higher transcript levels in wild plants. Rhizosphere microbiome analyses showed differences in bacterial and fungal community composition among the sampled groups. Exploratory cross-omics analysis identified candidate associations between several microbial taxa and terpenoid biosynthesis-related genes. Discussion: These taxonomic assignments do not establish the functional roles of the detected microorganisms. Because terpenoid and saponin concentrations were not measured, the transcriptomic differences do not demonstrate greater metabolite accumulation or improved medicinal quality. Moreover, because the populations were sampled from different sites and the microbiome data lacked independent biological replication within each sampling group, the observed patterns do not establish effects of cultivation status or habitat, nor do they demonstrate causal plant-microbe interactions. The results provide hypotheses for future controlled studies of